5 commits

Author	SHA1	Message	Date
SusiJo	2f3ddc90fb	added fasta_fai as input + changed if statements	2022-06-02 12:57:50 +02:00
SusiJo	f392c4bed5	removed params section & added description fasta	2022-05-20 13:05:43 +02:00
SusiJo	5a1297cc7d	added optional pdf/png outputs	2022-05-20 09:12:47 +02:00
Matthias Hörtenhuber	e745e167c1	Fix formatting in yaml files, add yamllint config (#1279) ... * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-02-15 11:15:27 +00:00
Florian De Temmerman	1455498152	CNVkit: Make targets file optional when running in WGS mode (#1030) ... * Make targets.bed optional when running in wgs mode * added test for cram * Update test_data_config with new reference.cnn * Update main.nf to allow tumor-only running Still need a unit-test for this. Almost ready, but needs this file as input https://github.com/nf-core/test-datasets/blob/modules/data/generic/cnn/reference.cnn * re-writing previous changes, but now it wont crash the entire CI-setup * fixing overlooked merge conflict * last overlooked merge-conflict * move all files to batch subfolder * adding an optional input for a reference file (needed when running germline and tumoronly) * minor typo * update meta.yml * aligning code, renaming cnvkit to cnvkit_batch, renaming tumorbam to tumor, normalbam to normal * Update pytest_modules.yml Co-authored-by: EC2 Default User <ec2-user@ip-172-31-21-198.us-west-2.compute.internal> Co-authored-by: Lasse Folkersen <lassefolkersen@gmail.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-11-21 19:56:57 +00:00

Renamed from modules/cnvkit/meta.yml (Browse further)